Objective: To investigate the association of special family structure and physical activity with psychological sub health among secondary vocational school students, so as to provide reference to inform mental health promotion in the population. Methods: From September to December 2024, a convenience sample was drawn from 16 schools including 5 141 secondary vocational school students across 8 provinces (municipalities) in China (Fujian, Chongqing, Guangdong, Guangxi, Hubei, Jiangxi, Shanghai, Zhejiang). A self developed questionnaire, Multidimensional Sub health Questionnaire of Adolescents and International Physical Activity Questionnaire Short Form were used to investigate and evaluate basic information, family structure, psychological sub health status and physical activity. Descriptive statistics and Logistic regression analysis were performed to explore relationships of special family structures and physical activity with psychological sub health in secondary vocational school students. Results: The detection rate of psychological sub health among secondary vocational school students was 11.0%. The reporting rates for secondary vocational school students who lost their father or lost their mother, whose parents divorced, whose parents remarried, and those from special family structures were 2.8%, 0.8%, 11.8%, 3.9%, and 14.7%, respectively. Moreover, the detection rates of psychological sub health and its sub dimensions significantly differed among secondary vocational school students grouped by family type (divorced parental families, remarried parental families and special family structures)( χ 2=5.90-22.67, all P <0.05). Binary Logistic regression indicated that maternal bereavement was associated with a higher risk of conduct problems [ AOR ( 95% CI )= 2.90(1.15-7.33)], and parental divorce was associated with a higher risk of psychological sub health ( AOR= 2.71 , 95%CI =1.04- 7.06 ) among secondary vocational school students (both P <0.05). Interaction analysis showed that both students with a special family structure and insufficient physical activity [ AOR (95% CI )=1.99(1.44-2.75)] and those with a non-special family structure and insufficient physical activity [ AOR (95% CI )=1.81(1.48-2.22)] were associated with increased risks of psychological sub health among secondary vocational school students (both P <0.01). Conclusion Special family structure and physical activity are associated with psychological sub health among secondary vocational school students; early identification and assessment based interventions for those with a special family structure should be strengthened, while school based physical activity should be implemented to increase physical activity levels,thereby reducing the risk of psychological sub health.